Molecular Ecology Resources最新文献

{"title":"Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment","authors":"Alexander Van?Nynatten,&nbsp;Kavishka S. Gallage,&nbsp;Nathan K. Lujan,&nbsp;Nicholas E. Mandrak,&nbsp;Nathan R. Lovejoy","doi":"10.1111/1755-0998.13803","DOIUrl":"https://doi.org/10.1111/1755-0998.13803","url":null,"abstract":"<p>Detection of invasive species is critical for management but is often limited by challenges associated with capture, processing and identification of early life stages. DNA metabarcoding facilitates large-scale monitoring projects to detect establishment early. Here, we test the use of DNA metabarcoding to monitor invasive species by sequencing over 5000 fishes in bulk ichthyoplankton samples (larvae and eggs) from four rivers of ecological and cultural importance in southern Canada. We were successful in detecting species known from each river and three invasive species in two of the four rivers. This includes the first detection of early life-stage rudd in the Credit River. We evaluated whether sampling gear affected the detection of invasive species and estimates of species richness, and found that light traps outperform bongo nets in both cases. We also found that the primers used for the amplification of target sequences and the number of sequencing reads generated per sample affect the consistency of species detections. However, these factors have less impact on detections and species richness estimates than the number of samples collected and analysed. Our analyses also show that incomplete reference databases can result in incorrectly attributing DNA sequences to invasive species. Overall, we conclude that DNA metabarcoding is an efficient tool for monitoring the early establishment of invasive species by detecting evidence of reproduction but requires careful consideration of sampling design and the primers used to amplify, sequence and classify the diversity of native and potentially invasive species.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1319-1333"},"PeriodicalIF":7.7,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13803","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5828095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference","authors":"Jonathan B. Puritz,&nbsp;Ximing Guo,&nbsp;Matthew Hare,&nbsp;Yan He,&nbsp;LaDeana W. Hillier,&nbsp;Shubo Jin,&nbsp;Ming Liu,&nbsp;Katie E. Lotterhos,&nbsp;Pat Minx,&nbsp;Tejashree Modak,&nbsp;Dina Proestou,&nbsp;Edward S. Rice,&nbsp;Chad Tomlinson,&nbsp;Wesley C. Warren,&nbsp;Erin Witkop,&nbsp;Honggang Zhao,&nbsp;Marta Gomez-Chiarri","doi":"10.1111/1755-0998.13801","DOIUrl":"10.1111/1755-0998.13801","url":null,"abstract":"<p>Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, <i>Crassostrea virginica</i>. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a <i>post hoc</i> method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9469211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)","authors":"André Gomes-dos-Santos,&nbsp;Elsa Froufe,&nbsp;John M. Pfeiffer,&nbsp;Nathan A. Johnson,&nbsp;Chase H. Smith,&nbsp;André M. Machado,&nbsp;L. Filipe C.?Castro,&nbsp;Van Tu Do,&nbsp;Akimasa Hattori,&nbsp;Nicole Garrison,&nbsp;Nathan V. Whelan,&nbsp;Ivan N. Bolotov,&nbsp;Ilya V. Vikhrev,&nbsp;Alexander V. Kondakov,&nbsp;Mohamed Ghamizi,&nbsp;Vincent Prié,&nbsp;Arthur E. Bogan,&nbsp;Manuel Lopes?Lima","doi":"10.1111/1755-0998.13802","DOIUrl":"https://doi.org/10.1111/1755-0998.13802","url":null,"abstract":"<p>The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and <i>de novo</i> assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1403-1422"},"PeriodicalIF":7.7,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13802","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5798911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP","authors":"Travis Seaborn,&nbsp;Erin L. Landguth,&nbsp;Christopher C. Caudill","doi":"10.1111/1755-0998.13799","DOIUrl":"https://doi.org/10.1111/1755-0998.13799","url":null,"abstract":"<p>Adaptive capacity can present challenges for modelling as it encompasses multiple ecological and evolutionary processes such as natural selection, genetic drift, gene flow and phenotypic plasticity. Spatially explicit, individual-based models provide an outlet for simulating these complex interacting eco-evolutionary processes. We expanded the existing Cost-Distance Meta-POPulation (CDMetaPOP) framework with inducible plasticity modelled as a habitat selection behaviour, using temperature or habitat quality variables, with a genetically based selection threshold conditioned on past individual experience. To demonstrate expected results in the new module, we simulated hypothetical populations and then evaluated model performance in populations of redband trout (<i>Oncorhynchus mykiss gairdneri</i>) across three watersheds where temperatures induce physiological stress in parts of the stream network. We ran simulations using projected warming stream temperature data under four scenarios for alleles that: (1) confer thermal tolerance, (2) bestow plastic habitat selection, (3) give both thermal tolerance and habitat selection preference and (4) do not provide either thermal tolerance or habitat selection. Inclusion of an adaptive allele decreased declines in population sizes, but this impact was greatly reduced in the relatively cool stream networks. As anticipated with the new module, high-temperature patches remained unoccupied by individuals with the allele operating plastically after exposure to warm temperatures. Using complete habitat avoidance above the stressful temperature threshold, habitat selection reduced the overall population size due to the opportunity cost of avoiding areas with increased, but not guaranteed, mortality. Inclusion of plasticity within CDMetaPOP will provide the potential for genetic or plastic traits and ‘rescue’ to affect eco-evolutionary dynamics for research questions and conservation applications.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1458-1472"},"PeriodicalIF":7.7,"publicationDate":"2023-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5725687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity","authors":"Nicolas C. Rochette,&nbsp;Angel G. Rivera-Colón,&nbsp;Jessica Walsh,&nbsp;Thomas J. Sanger,&nbsp;Shane C. Campbell-Staton,&nbsp;Julian M. Catchen","doi":"10.1111/1755-0998.13800","DOIUrl":"https://doi.org/10.1111/1755-0998.13800","url":null,"abstract":"<p>Library preparation protocols for most sequencing technologies involve PCR amplification of the template DNA, which open the possibility that a given template DNA molecule is sequenced multiple times. Reads arising from this phenomenon, known as PCR duplicates, inflate the cost of sequencing and can jeopardize the reliability of affected experiments. Despite the pervasiveness of this artefact, our understanding of its causes and of its impact on downstream statistical analyses remains essentially empirical. Here, we develop a general quantitative model of amplification distortions in sequencing data sets, which we leverage to investigate the factors controlling the occurrence of PCR duplicates. We show that the PCR duplicate rate is determined primarily by the ratio between library complexity and sequencing depth, and that amplification noise (including in its dependence on the number of PCR cycles) only plays a secondary role for this artefact. We confirm our predictions using new and published RAD-seq libraries and provide a method to estimate library complexity and amplification noise in any data set containing PCR duplicates. We discuss how amplification-related artefacts impact downstream analyses, and in particular genotyping accuracy. The proposed framework unites the numerous observations made on PCR duplicates and will be useful to experimenters of all sequencing technologies where DNA availability is a concern.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1299-1318"},"PeriodicalIF":7.7,"publicationDate":"2023-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13800","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5680175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant DNA barcode library for native flowering plants in the arid region of northwestern China","authors":"Feng Song,&nbsp;Ting Li,&nbsp;Hai-Fei Yan,&nbsp;Ying Feng,&nbsp;Lu Jin,&nbsp;Kevin S. Burgess,&nbsp;Xue-Jun Ge","doi":"10.1111/1755-0998.13797","DOIUrl":"https://doi.org/10.1111/1755-0998.13797","url":null,"abstract":"<p>DNA barcoding is a well-established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographical regions. The arid region in northwestern China, a vast area of about 2.5 million km², is ecologically fragile and often overlooked in biodiversity studies. In particular, DNA barcode data from the arid region in China are lacking. We develop and evaluate the efficacy of an extensive DNA barcode library for native flowering plants in the arid region of northwestern China. Plant specimens were collected, identified and vouchered for this purpose. The database utilized four DNA barcode markers, namely <i>rbcL</i>, <i>matK</i>, ITS and ITS2, for 1816 accessions (representing 890 species from 385 genera and 72 families), and consisted of 5196 barcode sequences. Individual barcodes varied in resolution rates: species- and genus-level rates for <i>rbcL</i>, <i>matK</i>, ITS and ITS2 were 79.9%–51.1%/76.1%, 79.9%–67.2%/88.9%, 85.0%–72.0%/88.2% and 81.0%–67.4%/84.9%, respectively. The three-barcode combination of <i>rbcL</i> + <i>matK</i> + ITS (RMI) revealed a higher species- and genus-level resolution (75.5%/92.1%, respectively). A total of 110 plastomes were newly generated as super-barcodes to increase species resolution for seven species-rich genera, namely <i>Astragalus</i>, <i>Caragana</i>, <i>Lactuca</i>, <i>Lappula</i>, <i>Lepidium</i>, <i>Silene</i> and <i>Zygophyllum</i>. Plastomes revealed higher species resolution compared to standard DNA barcodes and their combination. We suggest future databases include super-barcodes, especially for species-rich and complex genera. The plant DNA barcode library in the current study provides a valuable resource for future biological investigations in the arid regions of China.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1389-1402"},"PeriodicalIF":7.7,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6107661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron","authors":"Eva Sandoval-Quintana,&nbsp;Christina Stangl,&nbsp;Lionel Huang,&nbsp;Ivo Renkens,&nbsp;Robert Duran,&nbsp;Gijs van Haaften,&nbsp;Glen Monroe,&nbsp;Béatrice Lauga,&nbsp;Christine Cagnon","doi":"10.1111/1755-0998.13798","DOIUrl":"https://doi.org/10.1111/1755-0998.13798","url":null,"abstract":"<p>Environmental integrons are ubiquitous in natural microbial communities, but they are mostly uncharacterized and their role remains elusive. Thus far, research has been hindered by methodological limitations. Here, we successfully used an innovative approach combining CRISPR-Cas9 enrichment with long-read nanopore sequencing to target, in a complex microbial community, a putative adaptive environmental integron, InOPS, and to unravel its complete structure and genetic context. A contig of 20 kb was recovered containing the complete integron from the microbial metagenome of oil-contaminated coastal sediments. InOPS exhibited typical integron features. The integrase, closely related to integrases of marine Desulfobacterota, possessed all the elements of a functional integron integrase. The gene cassettes harboured mostly unknown functions hampering inferences about their ecological importance. Moreover, the putative InOPS host, likely a hydrocarbonoclastic marine bacteria, raises questions as to the adaptive potential of InOPS in response to oil contamination. Finally, several mobile genetic elements were intertwined with InOPS highlighting likely genomic plasticity, and providing a source of genetic novelty. This case study showed the power of CRISPR-Cas9 enrichment to elucidate the structure and context of specific DNA regions for which only a short sequence is known. This method is a new tool for environmental microbiologists working with complex microbial communities to target low abundant, large or repetitive genetic structures that are difficult to obtain by classical metagenomics. More precisely, here, it offers new perspectives to comprehensively assess the eco-evolutionary significance of environmental integrons.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1288-1298"},"PeriodicalIF":7.7,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5642493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Landscape transcriptomics as a tool for addressing global change effects across diverse species.","authors":"Jason Keagy,&nbsp;Chloe P Drummond,&nbsp;Kadeem J Gilbert,&nbsp;Christina M Grozinger,&nbsp;Jill Hamilton,&nbsp;Heather M Hines,&nbsp;Jesse Lasky,&nbsp;Cheryl A Logan,&nbsp;Ruairidh Sawers,&nbsp;Tyler Wagner","doi":"10.1111/1755-0998.13796","DOIUrl":"https://doi.org/10.1111/1755-0998.13796","url":null,"abstract":"<p><p>Landscape transcriptomics is an emerging field studying how genome-wide expression patterns reflect dynamic landscape-scale environmental drivers, including habitat, weather, climate, and contaminants, and the subsequent effects on organismal function. This field is benefitting from advancing and increasingly accessible molecular technologies, which in turn are allowing the necessary characterization of transcriptomes from wild individuals distributed across natural landscapes. This research is especially important given the rapid pace of anthropogenic environmental change and potential impacts that span levels of biological organization. We discuss three major themes in landscape transcriptomic research: connecting transcriptome variation across landscapes to environmental variation, generating and testing hypotheses about the mechanisms and evolution of transcriptomic responses to the environment, and applying this knowledge to species conservation and management. We discuss challenges associated with this approach and suggest potential solutions. We conclude that landscape transcriptomics has great promise for addressing fundamental questions in organismal biology, ecology, and evolution, while providing tools needed for conservation and management of species.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9300583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taking eDNA underground: Factors affecting eDNA detection of subterranean fauna in groundwater","authors":"Mieke van der Heyde,&nbsp;Nicole E. White,&nbsp;Paul Nevill,&nbsp;Andrew D. Austin,&nbsp;Nicholas Stevens,&nbsp;Matt Jones,&nbsp;Michelle T. Guzik","doi":"10.1111/1755-0998.13792","DOIUrl":"https://doi.org/10.1111/1755-0998.13792","url":null,"abstract":"<p>Stygofauna are aquatic fauna that have evolved to live underground. The impacts of anthropogenic climate change, extraction and pollution on groundwater pose major threats to groundwater health, prompting the need for efficient and reliable means to detect and monitor stygofaunal communities. Conventional survey techniques for these species rely on morphological identification and can be biased, labour-intensive and often indeterminate to lower taxonomic levels. By contrast, environmental DNA (eDNA)-based methods have the potential to dramatically improve on existing stygofaunal survey methods in a large range of habitats and for all life stages, reducing the need for the destructive manual collection of often critically endangered species or for specialized taxonomic expertise. We compared eDNA and haul-net samples collected in 2020 and 2021 from 19 groundwater bores and a cave on Barrow Island, northwest Western Australia, and assessed how sampling factors influenced the quality of eDNA detection of stygofauna. The two detection methods were complementary; eDNA metabarcoding was able to detect soft-bodied taxa and fish often missed by nets, but only detected seven of the nine stygofaunal crustacean orders identified from haul-net specimens. Our results also indicated that eDNA metabarcoding could detect 54%–100% of stygofauna from shallow-water samples and 82%–90% from sediment samples. However, there was significant variation in stygofaunal diversity between sample years and sampling types. The findings of this study demonstrate that haul-net sampling has a tendency to underestimate stygofaunal diversity and that eDNA metabarcoding of groundwater can substantially improve the efficiency of stygofaunal surveys.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1257-1274"},"PeriodicalIF":7.7,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13792","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5908707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages","authors":"A. Bush,&nbsp;Z. Compson,&nbsp;N. K. Rideout,&nbsp;B. Levenstein,&nbsp;M. Kattilakoski,&nbsp;M. Hajibabaei,&nbsp;W. A. Monk,&nbsp;M. T. G. Wright,&nbsp;D. J. Baird","doi":"10.1111/1755-0998.13794","DOIUrl":"https://doi.org/10.1111/1755-0998.13794","url":null,"abstract":"<p>The delivery of consistent and accurate fine-resolution data on biodiversity using metabarcoding promises to improve environmental assessment and research. Whilst this approach is a substantial improvement upon traditional techniques, critics note that metabarcoding data are suitable for establishing taxon occurrence, but not abundance. We propose a novel hierarchical approach to recovering abundance information from metabarcoding, and demonstrate this technique using benthic macroinvertebrates. To sample a range of abundance structures without introducing additional changes in composition, we combined seasonal surveys with fish-exclusion experiments at Catamaran Brook in northern New Brunswick, Canada. Five monthly surveys collected 31 benthic samples for DNA metabarcoding divided between caged and control treatments. A further six samples per survey were processed using traditional morphological identification for comparison. By estimating the probability of detecting a single individual, multispecies abundance models infer changes in abundance based on changes in detection frequency. Using replicate detections of 184 genera (and 318 species) from metabarcoding samples, our analysis identified changes in abundance arising from both seasonal dynamics and the exclusion of fish predators. Counts obtained from morphological samples were highly variable, a feature that limited the opportunity for more robust comparison, and emphasizing the difficulty standard methods also face to detect changes in abundance. Our approach is the first to demonstrate how quantitative estimates of abundance can be made using metabarcoding, both among species within sites as well as within species among sites. Many samples are required to capture true abundance patterns, particularly in streams where counts are highly variable, but few studies can afford to process entire samples. Our approach allows study of responses across whole communities, and at fine taxonomic resolution. We discuss how ecological studies can use additional sampling to capture changes in abundance at fine resolution, and how this can complement broad-scale biomonitoring using DNA metabarcoding.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"23 6","pages":"1275-1287"},"PeriodicalIF":7.7,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13794","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5906886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}